We just finished our hatch yesterday.
I did use a carton after using an auto turner. In the home stretch I ended up removing them from the carton as it seemed gravity could actually help them hatch and I think it was easier once they had zipped a bit of the shell. Not really sure because it was our first hatch and I think I was just impatient and worried.
As for the wrong end pip, I remember reading that someone else dealt with that on BYC but I can't find the thread so I can't remember the recommendations or outcome. Sorry.
We did lose on the day before hatch day.
The shell had gone dark and blotchy from the inside and then the 'ling wasn't moving anymore.
The rest of them are doing great.
Good luck with your hatch.
kwack